Whatever fits your workflow most comfortably.
Personally I don't bother with "exact fit" hitboxes, so creating a rectangular box in Construct's editor is no problem for me. For that matter, I only ever have to make one since it's just a rectangle and I can shape and size it during runtime, and they all serve the same purpose.
If you want to paint exact hitboxes, it might be more comfortable to do so with your image editor of choice, with the ability to use layers, transparencies, brushes, and bulk export options. Again, I'd say that this isn't standard practice, and is probably going to cause more problems and headaches than it's worth...